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Copier update: pyrefly - #71
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Resolves the remaining explicit-any errors, leaving pyrefly at 0. src is now free of Any entirely: - the XML payload dicts threaded through the step classes become dict[str, JsonValue], which is what they actually are on their way to json.dumps - WORKING_DIRECTION_KWARGS and volume_info drop their annotations so the type is inferred rather than asserted - model_post_init's discarded parameter widens to object The three remaining sites are test-only. They build a dict of kwargs to spread into a pydantic constructor, omitting entries so the constructor defaults get exercised, so the value type is heterogeneous by construction. dict[str, object] is rejected on the unpack and a TypedDict cannot be built from a comprehension, so these carry an inline pyrefly suppression instead.
The dependency swap to types-lxml changed pyproject.toml and uv.lock, which are part of the devcontainer build context.
The parameter is a list of selection payloads, each containing a Wells list alongside the deck section, spacing and working direction --- not the single well that the identically named parameters on _add_mix_group and _create_heights_value_tuple receive. It is serialized under the MultiSelection key, so name it for that.
…election Each of these locals has exactly one use, as the multi_selection argument to _add_location_group. Naming them for what they are keeps the two halves of that call consistent.
…mage
hadolint v2.15.1, which the template update pins, adds DL3066: a
username may not be resolvable by the host system, so a UID is
preferred. v2.14.0 did not report this.
root is UID 0, so the build is unchanged. This switch is build-time
only --- the final USER remains ${NB_USER} at UID 1000, which is what
repo2docker requires of the image's primary user.
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Pull request overview
Updates the repository’s Copier templates and migrates source type checking from Pyright to Pyrefly.
Changes:
- Adds Pyrefly configuration and resolves typing errors.
- Updates template-managed CI, release, development, and agent tooling.
- Adds mutation-testing utilities and dependency updates.
Template-managed fixes should be applied to the owning base or Python-package template and re-synced.
Reviewed changes
Copilot reviewed 129 out of 132 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
ty.toml |
Removes obsolete type-checker configuration. |
tests/unit/method_steps/test_simple_transfer.py |
Updates lint and Pyrefly suppressions. |
tests/unit/method_steps/test_multi_dispense.py |
Updates lint and Pyrefly suppressions. |
tests/unit/conftest.py |
Adds template ownership notice. |
tests/unit/__init__.py |
Establishes the unit-test package. |
tests/conftest.py |
Registers assertion rewriting. |
tests/__init__.py |
Establishes the test package. |
src/pyalab/steps/transfer.py |
Refines payload types and naming. |
src/pyalab/steps/set_volume.py |
Removes unnecessary Any annotation. |
src/pyalab/steps/params.py |
Uses relative imports. |
src/pyalab/steps/multi_dispense.py |
Refines payload types and naming. |
src/pyalab/steps/builders.py |
Uses JsonValue and relative imports. |
src/pyalab/steps/base.py |
Adds Pyrefly-compatible state and payload types. |
src/pyalab/steps/__init__.py |
Declares intentional exports. |
src/pyalab/program.py |
Removes stale suppression and Any. |
src/pyalab/integra_xml.py |
Expands filtering for branch coverage. |
sh.bat |
Adds template ownership notice. |
scripts/delete_false_positive_rej.py |
Adds template ownership notice. |
README.md |
Documents release and Copier workflows. |
pytest.ini |
Points coverage at the relocated configuration. |
pyrightconfig.json |
Restricts Pyright to consumer-style test checking. |
pyproject.toml |
Updates typing, testing, and mutation dependencies. |
LICENSE |
Adds template ownership notice. |
docs/requirements.txt |
Adds template ownership notice. |
docs/Makefile |
Adds template ownership notice. |
docs/make.bat |
Adds template ownership notice. |
docs/index.rst |
Adds template ownership notice. |
docs/conf.py |
Updates callback lint suppression. |
docs/_static/.gitkeep |
Adds template ownership notice. |
Dockerfile |
Uses numeric root UID. |
CLAUDE.md |
Removes superseded root configuration. |
CHANGELOG.md |
Adds template ownership notice. |
biome.jsonc |
Adds template ownership notice. |
AGENTS.md |
Expands development and review guidance. |
.readthedocs.yaml |
Adds template ownership notice. |
.python-version |
Updates generated formatting. |
.pre-commit-config.yaml |
Adds Pyrefly and updates hooks/config paths. |
.gitignore |
Ignores mutation output. |
.github/workflows/release.yaml |
Adds the consolidated release workflow. |
.github/workflows/publish.yaml |
Updates actions and tag handling. |
.github/workflows/publish_to_staging.yaml |
Updates action versions. |
.github/workflows/pre-commit.yaml |
Reworks pre-commit caching. |
.github/workflows/hash_git_files.py |
Normalizes line endings while hashing. |
.github/workflows/git_tag.py |
Separates version extraction from tagging. |
.github/workflows/get-values.yaml |
Safely handles merge messages. |
.github/workflows/extract_project_version.py |
Adds reusable version extraction. |
.github/workflows/confirm-on-tagged-copier-template.yaml |
Updates checkout action. |
.github/workflows/ci.yaml |
Builds and stores release artifacts. |
.github/pull_request_template.md |
Adds template ownership notice. |
.github/ISSUE_TEMPLATE/tech-debt.yml |
Adds template ownership notice. |
.github/ISSUE_TEMPLATE/feature-request.yml |
Adds template ownership notice. |
.github/ISSUE_TEMPLATE/config.yml |
Adds template ownership notice. |
.github/ISSUE_TEMPLATE/bug-report.yml |
Adds template ownership notice. |
.github/dependabot.yml |
Adds template ownership notice. |
.github/CONTRIBUTING.md |
Corrects links and adds ownership notice. |
.github/CODE_OF_CONDUCT.md |
Adds template ownership notice. |
.github/actions/update-devcontainer-hash/action.yml |
Updates checkout action. |
.github/actions/install_deps/action.yml |
Modernizes Python, Node, and pnpm setup. |
.github/actions/ecr-auth/action.yml |
Updates AWS actions. |
.github/actions/check-skip-duplicates/action.yml |
Adds template ownership notice. |
.github/.codecov.yml |
Adds template ownership notice. |
.devcontainer/windows-host-helper.sh |
Adds template ownership notice. |
.devcontainer/post-start-command.sh |
Adds template ownership notice. |
.devcontainer/on-create-command.sh |
Allows uv-managed Python installation. |
.devcontainer/on-create-command-boilerplate.sh |
Adds template ownership notice. |
.devcontainer/manual-setup-deps.py |
Adds template ownership notice. |
.devcontainer/install-ci-tooling.py |
Updates development tool versions. |
.devcontainer/initialize-command.sh |
Adds template ownership notice. |
.devcontainer/Dockerfile |
Adds template ownership notice. |
.devcontainer/docker-compose.yml |
Adds template ownership notice. |
.devcontainer/devcontainer.json |
Configures Pyrefly and updates extensions. |
.devcontainer/create-aws-profile.sh |
Adds template ownership notice. |
.devcontainer/code-artifact-auth.sh |
Adds template ownership notice. |
.config/ruff.toml |
Relocates cache and expands coverage-oriented rules. |
.config/ruff-non-src.toml |
Adds template ownership notice. |
.config/pyrefly.toml |
Configures project-wide Pyrefly checking. |
.config/pyrefly.mutmut.toml |
Configures mutation type checking. |
.config/pylintrc.toml |
Adds ownership and spelling directives. |
.config/.prettierrc |
Adds shared formatting configuration. |
.config/.coveragerc |
Updates Pyrefly terminology and ownership. |
.config/.copier-managed-files.json |
Records template file ownership. |
.config/.copier-answers.yml |
Advances the Copier template version. |
.config/_typos.toml |
Updates spell-check configuration. |
.coderabbit.yaml |
Updates review guidance for Pyrefly and Copier. |
.claude/skills/fix-mutants/verify-mutant.py |
Adds single-mutant verification. |
.claude/skills/fix-mutants/utils.py |
Adds shared mutation utilities. |
.claude/skills/fix-mutants/SKILL.md |
Defines the mutation-testing workflow. |
.claude/skills/fix-mutants/show-mutant.py |
Adds mutant inspection output. |
.claude/skills/fix-mutants/run-mutmut.py |
Adds mutation-suite execution. |
.claude/skills/fix-mutants/list-survived.py |
Lists actionable mutants. |
.claude/skills/fix-mutants/group-by-line.py |
Groups mutants by source line. |
.claude/skills/fix-mutants/check-results.py |
Detects prior mutation results. |
.claude/skills/caveman/SKILL.md |
Adds template ownership notice. |
.claude/skills/address-pr-comments/verify-env.py |
Adds environment and PR validation. |
.claude/skills/address-pr-comments/utils.py |
Adds shared command execution. |
.claude/skills/address-pr-comments/SKILL.md |
Refines the PR-comment workflow. |
.claude/skills/address-pr-comments/post-reply.py |
Reuses shared command handling. |
.claude/skills/address-pr-comments/fetch-pr-comments.py |
Forces UTF-8 subprocess decoding. |
.claude/skills/address-pr-comments/commit-link.py |
Generates commit links for replies. |
.claude/skills/address-pr-comments/check-footer.py |
Adds template ownership notice. |
.claude/settings/permissions/write.jsonc |
Adds template ownership notice. |
.claude/settings/permissions/read.jsonc |
Adds template ownership notice. |
.claude/settings/permissions/bash.jsonc |
Broadens Git permissions with safeguards. |
.claude/settings/permissions/additional-dirs.jsonc |
Adds template ownership notice. |
.claude/settings/models.jsonc |
Defines available models. |
.claude/settings/hooks.jsonc |
Adds template ownership notice. |
.claude/settings/basics.jsonc |
Adds template ownership notice. |
.claude/hooks/caveman-mode-tracker.js |
Adds template ownership notice. |
.claude/hooks/caveman-config.js |
Adds template ownership notice. |
.claude/hooks/caveman-activate.js |
Adds template ownership notice. |
.claude/hooks/bash-chain-guard.js |
Expands command-chain detection. |
.claude/helpers/merge-claude-settings.sh |
Adds template ownership notice. |
.claude/commands/tdd.md |
Refines one-behavior TDD guidance. |
.claude/commands/tdd-review.md |
Refines test-smell criteria. |
.claude/commands/summarize.md |
Adds template ownership notice. |
.claude/commands/spike.md |
Refines one-behavior TDD guidance. |
.claude/commands/simplify.md |
Adds template ownership notice. |
.claude/commands/research.md |
Adds template ownership notice. |
.claude/commands/refactor.md |
Refines one-behavior TDD guidance. |
.claude/commands/red.md |
Refines one-behavior TDD guidance. |
.claude/commands/polish.md |
Adds template ownership notice. |
.claude/commands/issue.md |
Refines one-behavior TDD guidance. |
.claude/commands/green.md |
Refines one-behavior TDD guidance. |
.claude/commands/gap.md |
Adds template ownership notice. |
.claude/commands/create-issues.md |
Adds template ownership notice. |
.claude/commands/create-adr.md |
Adds template ownership notice. |
.claude/commands/commit.md |
Adds template ownership notice. |
.claude/commands/add-command.md |
Adds template ownership notice. |
.claude/CLAUDE.md |
Redirects Claude guidance to AGENTS.md. |
.claude/.beads/config.yaml |
Adds template ownership notice. |
.claude/.beads/.gitignore |
Adds template ownership notice. |
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Why is this change necessary?
Update do use pyrefly
How does this change address the issue?
Two distinct parts.
1. Template sync — the bulk of the diff, applied from
copier-base-template. Mostly generated; the files it owns are listed in.config/.copier-managed-files.json.2. Making the codebase pass pyrefly — 45 errors, in five groups:
bad-assignment,bad-argument-type,bad-returnlxml-stubs0.5.1 declares attributes with PEP 484 type comments (text = ... # type: Optional[str]), which pyrefly does not read, so it inferred_Element.textasEllipsistypes-lxmlexplicit-anydict[str, Any]on the XML payload dicts threaded through the step classespydantic.JsonValue,object, or dropped annotationsimplicit-reexportsrc/pyalab/steps/__init__.pyre-exported without declaring intent__all__bad-argument-typesteps/*.pyimported the package absolutely (from pyalab.plate import ...) while the rest ofsrcused relative imports, so one class resolved under two module names and read as two nominal typesimplicit-bool,implicitly-defined-attribute,unused-type-ignoreis not Noneloop, declared private attr, deleted a stale pyright ignoreResult: pyrefly reports 0 errors, with 3 suppressions (see below).
Two naming fixes came out of reading the code closely, both pure renames with no type or behavior change:
_add_location_group'swell_info→multi_selection. ThreeStepmethods took awell_infoparameter; two received a single well ({Item1, Item2}) while this one received a list of selection payloads that merely contain a wells list. It serializes under the XML keyMultiSelection, so it is now named for that.source_info/target_infolocals →source_selection/target_selection.Separately, 3 pre-existing
PLR0917ruff violations are fixed. Each already carried a deliberate# noqa: PLR0913;PLR0917is that rule's sibling for positional argument count and was never suppressed. All three genuinely cannot go keyword-only (a Sphinx callback signature, and two parametrized tests), so the existing noqa was extended with reasoning.What side effects does this change have?
lxml-stubs→types-lxmlpulls intypes-html5lib,types-webencodings,cssselect,soupsieve,beautifulsoup4. All dev-only; runtime dependencies are unchanged. Worth notinglxml-stubs0.5.1 is the latest release and dates from 2024-01-10, whereastypes-lxmlis actively maintained.src. If you rely on pyright diagnostics in the editor for library code, that is now pyrefly's job..config/. Anything invoking these tools directly needs the new paths;pre-commit run <hook-id>handles it already.dict[str, object]is rejected on the unpack and aTypedDictcannot be built from a comprehension, so neither alternative works.src/itself contains noAnyand no suppressions.How is this change tested?
Existing CI